RNA Analysis Enables Resolution and Reclassification of Reportedly Benign Synonymous Variants

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Synonymous variants, previously considered neutral, can impact RNA processing and protein function.
• Accurate variant classification is crucial for clinical diagnosis and treatment strategies.
• Exome sequencing identifies variants, but functional validation, especially RNA splicing, is often needed.

Purpose of the Study:

• To investigate the functional impact of synonymous variants on RNA splicing.
• To re-evaluate the clinical significance of variants initially classified as "likely benign."
• To emphasize the importance of RNA-based testing in variant interpretation.

Main Methods:

• Exome sequencing to detect synonymous variants.
• Segregation analysis within families to correlate variants with phenotypes.
• RNA studies (e.g., RT-PCR) to detect splicing alterations like exon skipping.

Main Results:

• Three synonymous variants in LARS1, POLE, and COL2A1 were identified.
• Two variants, initially "likely benign" in ClinVar, showed significant exon skipping.
• Segregation analysis confirmed the association of variants with disease phenotypes.
• Reclassification of variants to "likely pathogenic" based on RNA splicing defects.

Conclusions:

• Synonymous variants can act as pathogenic variants by disrupting RNA splicing.
• RNA-based functional studies are essential for accurate variant classification and clinical management.
• Integrating RNA analysis improves diagnostic yield and therapeutic decision-making for genetic disorders.